Indonesia is at the center of the world’s marine biodiversity, with 76% of the world’s coral reef species and 37% of the world’s coral reef fish species. This biodiversity is critical to support the healthy functioning of Indonesia’s marine ecosystems, so they are resilient to adapt to ecological changes from climate or human impacts. Indonesia also ranks as the second largest fish producer in the world, producing 5.4 million tons of fish in 2012. But many of its fisheries are over taxed and in decline. In order to sustain or increase this level of fish production for Indonesia’s food security and economy without causing irreparable damage to the marine ecosystem, all stakeholders need to work together to increase ecosystem-based management of fisheries, especially in biologically significant marine areas.